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.TH FPOCKET 1 "JANUARY 2009" Linux "User Manuals"
.SH NAME
fpocket \- find pockets in proteins
.SH SYNOPSIS
.B fpocket -f
.I pdb-file
.B [OPTIONS]

.B fpocket -F
.I pdb-list
.B [OPTIONS]

.SH DESCRIPTION
.B fpocket
is a program that performs pocket detection on a protein structure. 
It uses (a this time) a geometric algorithm based on the Voronoi
tesselation.

.B fpocket 
uses qhull to perform the Voronoi tesselation. Make sure you 
have installed qhull and qvoronoi is accessible through the 
command line typing qvoronoi in your console.
Qhull can be downloaded from http://www.qhull.org

The -f option is needed, as it provide the input pdb file.
One can use -F option instead, to profide a list of pdb file
instead of a single one.

.SH OPTIONS

.IP -m 
.I minr 
.B [float]

Minimum radius criteria for alpha sphere selection. The qhull program
returns a large set of alpha sphere calculated on the protein. Not all
of them are necessary to perform the cavity detection. Besides, taking
all of them would dramatically decrease algorithm's speed.

.B DEFAULT: 3.0

.IP -M
.I maxr 
.B [float]

Maximum radius criteria for alpha sphere selection.

.B DEFAULT: 6.0

.IP -i 
.I nmin 
.B [integer]

Minimum number of alpha spheres for each pocket. When the clustering is
done, all pockets containing N <= 
.I nmin 
alpha sphere will be removed.

.B DEFAULT: 36

.IP -D 
.I mina 
.B [float]

The first basic clustering algorithm distance criteria. Alpha spheres
separated by a distance lower or equal than 
.I cdist 
to each others will be regrouped during this first clustering step.

.B DEFAULT: 1.73

.IP -r
.I bdist 
.B [float]

Distance criteria for the last clustering step. Given two groups of alpha spheres
already clustered with the basic algorithm, if barycenters of the two groups 
are distant of less than 
.I bdist 
from each other, the two groups are merged.

.B DEFAULT: 4.5

.IP -s
.I sdist [float]
The single-linkage distance criteria. Given two group of alpha sphere
already regrouped by the first two clustering steps, 
if 
.I snb 
(see -n option bellow) alpha spheres are separated by a distance 
lower than 
.I sdist, 
merge the two groups.

.B DEFAULT: 2.5

.IP -n 
.I snb 
.B [float]

Number of common vertices criteria for the single linkage algorithm.
Given two group of alpha sphere. If the number of vertice separated by 
a distance lower than s (given by the -s option) is greater or equal 
to the number given by this option, just merge the two groups.

.B DEFAULT: 3

.IP -A
.I anb 
.B [integer]
An alpha sphere will be considered as apolar if it has at least 
.I anb 
atoms neighbours (4 max. then) having an electronegativity value 
lower than 2.7 (using the Pauling representation).

.B DEFAULT: 3

.IP -p
.I minap 
.B [integer]

Minimum number of apolar alpha spheres for each pocket. If a given pocket has a
number of apolar alpha shape bellow
.I minap
, it will be removed.

.B DEFAULT: 0

.IP -v
.I mcvol 
.B [integer]

Number of Monte Carlo iterations for the volume estimation. The more this value is
high, the more the volume estimation will be accurate, and of course the more the 
program will be slow. This is the default method used to estimate the volume.

.B DEFAULT: 2500

.IP -b
.I dvol 
.B [integer]

This option allows the user to chose a discrete algorithm to calculate the volume of
each pocket instead of the Monte Carlo method. This algorithm put each pocket into 
a grid of dimention (1/N*X ; 1/N*Y ; 1/N*Z), N being the value given using this option,
and X, Y and Z are the box dimensions, determined from extreme coordinates of vertices.
Then, a triple iteration on each dimensions is used to estimate the volume, checking if
each points given by the iteration is in one of the pocket's vertices. 

.B Warning: 
a high value might dramatically slow down the programm, as this algorithm 
has a maximum complexity of N*N*N*nb_vertices, and a minimum of N*N*N. !!!

.B DEFAULT: Not used by default.

.SH BUGS
.SH AUTHOR
.BR Developpers:

Peter Schmidtke <pschmidtke@mmb.pcb.ub.es>

Vincent Le Guilloux <vincent.le-guilloux@univ-orleans.fr>

.BR Supervisor:

Pierre Tuffery

.SH "SEE ALSO"
.BR dpocket (1),
.BR tpocket (1),
